#EXTRA_DIST =  batman.ini 
AM_CFLAGS = -w -O3 -funroll-loops -maccumulate-outgoing-args -msse2 -lm -pthread
AM_CXXFLAGS = -w -O3 -funroll-loops -maccumulate-outgoing-args -msse2 -lm -pthread
RANLIB=ranlib
#AM_CPPFLAGS = -O3 -funroll-loops -maccumulate-outgoing-args -msse2 -lm

dist_bin_SCRIPTS = build_index bwtformatdb filter ann2loc.pl reverse
noinst_LIBRARIES = libz.a
libz_a_SOURCES = adler32.c compress.c crc32.c gzio.c uncompr.c deflate.c trees.c \
       zutil.c inflate.c infback.c inftrees.c inffast.c\
       zlib.h zconf.h crc32.h  deflate.h zutil.h inftrees.h inflate.h inffast.h trees.h inffixed.h
bin_PROGRAMS = index penguin-s penguin 
index_SOURCES= bfix.cpp index.cpp BWT.c MiscUtilities.c MemManager.c TextConverter.c r250.c QSufSort.c\
 iniparser.c inistrlib.c dictionary.c DNACount.c Timing.c Socket.c HSP.c HSPstatistic.c karlin.c\
 BWT.h TypeNLimit.h MemManager.h TextConverter.h HSP.h MiscUtilities.h DNACount.h r250.h HSPstatistic.h\
 BWTConstruct.h QSufSort.h r250.h dictionary.h inistrlib.h iniparser.h Timing.h Socket.h karlin.h\
 bfix.h 
penguin_s_SOURCES = print-s.cpp filters-s.cpp utils-s.cpp batlib-s.cpp rqindex-s.cpp penguin-s.cpp map-s.cpp ssw.h command.h global.h swroutines-s.h kseq.h\
 bfix.cpp BWT.c MiscUtilities.c MemManager.c TextConverter.c r250.c QSufSort.c ssw.c command-s.cpp swroutines-s.cpp\
 iniparser.c inistrlib.c dictionary.c DNACount.c Timing.c Socket.c HSP.c HSPstatistic.c karlin.c fastsw-s.cpp\
 print-s.h filters.h BWT.h TypeNLimit.h MemManager.h TextConverter.h HSP.h MiscUtilities.h DNACount.h r250.h HSPstatistic.h\
 BWTConstruct.h QSufSort.h r250.h dictionary.h inistrlib.h iniparser.h Timing.h Socket.h karlin.h\
 bfix.h rqindex.h utils.h batlib.h common.h map.h fastsw.h
penguin_SOURCES = print.cpp filters.cpp utils.cpp batlib.cpp rqindex.cpp penguin.cpp map.cpp ssw.h command.h global.h swroutines.h kseq.h\
 bfix.cpp BWT.c MiscUtilities.c MemManager.c TextConverter.c r250.c QSufSort.c ssw.c command.cpp swroutines.cpp\
 iniparser.c inistrlib.c dictionary.c DNACount.c Timing.c Socket.c HSP.c HSPstatistic.c karlin.c fastsw.cpp\
 print.h filters.h BWT.h TypeNLimit.h MemManager.h TextConverter.h HSP.h MiscUtilities.h DNACount.h r250.h HSPstatistic.h\
 BWTConstruct.h QSufSort.h r250.h dictionary.h inistrlib.h iniparser.h Timing.h Socket.h karlin.h\
 bfix.h rqindex.h utils.h batlib.h common.h map.h fastsw.h
#batman_SOURCES= batman.cpp BWT.c BWTConstruct.c MiscUtilities.c MemManager.c TextConverter.c r250.c QSufSort.c\
# iniparser.c inistrlib.c dictionary.c DNACount.c Timing.c Socket.c HSP.c HSPstatistic.c karlin.c 
#batman_LDADD = libz.a
#decode_SOURCES= decode.cpp BWT.c BWTConstruct.c MiscUtilities.c MemManager.c TextConverter.c r250.c QSufSort.c\
# iniparser.c inistrlib.c dictionary.c DNACount.c Timing.c Socket.c HSP.c HSPstatistic.c karlin.c
#decode_LDADD = libz.a
#reverse_SOURCES = reverse.cpp 
#copy:
#	cp bwtformatdb ../bin
#	cp reverse ../bin
#	cp batman ../bin
#	cp decode ../bin
